Contacts of the helix formed by residues 45 - 60 (chain A) in PDB entry 2R6C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A GLU* 3.6 6.7 + - - +
18A GLN* 5.0 5.2 - - - +
43A PHE* 3.5 6.3 - - - +
44A TYR* 1.3 88.4 - - + +
46A ALA* 1.3 61.7 + - - +
47A ALA* 3.4 6.7 - - + +
48A HIS* 3.3 35.5 + - + +
49A GLN* 3.0 21.0 + - - +
88A TYR* 4.1 21.0 + - - -
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR 3.7 2.8 + - - -
45A ARG* 1.3 68.8 - - - +
47A ALA* 1.3 57.5 + - - +
48A HIS 3.0 1.3 - - - -
49A GLN* 2.8 18.7 + - + +
50A LYS* 2.7 54.8 + - - +
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ARG* 5.1 7.0 - - + -
46A ALA* 1.3 79.2 - - - +
48A HIS* 1.3 65.6 + - + +
50A LYS* 3.4 11.5 + - - +
51A ILE* 3.1 32.2 + - - +
82A GLU 4.6 3.8 - - - +
83A ILE* 3.5 35.9 - - + +
88A TYR* 5.2 2.5 - - + -
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLU 6.2 0.2 - - - -
17A GLU* 2.8 42.9 + - + +
18A GLN* 3.8 20.2 - - + -
21A LEU* 3.7 21.0 - - + +
43A PHE* 3.5 13.2 - - + -
45A ARG* 3.3 25.0 + - + +
46A ALA 3.0 0.6 - - - -
47A ALA* 1.3 80.5 - - + +
49A GLN* 1.3 65.5 + - - +
50A LYS 3.2 0.2 - - - -
51A ILE* 3.7 1.6 - - + +
52A PHE* 2.9 28.1 + - - +
88A TYR* 2.4 44.4 + + - -
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Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.1 38.8 - - + +
41A GLU* 3.8 25.4 + - - +
43A PHE* 3.1 20.9 - - - +
44A TYR 4.2 2.9 - - - +
45A ARG 3.0 11.6 + - - +
46A ALA* 2.8 23.3 + - + +
48A HIS* 1.3 76.5 - - - +
50A LYS* 1.3 55.3 + - + +
53A HIS* 3.0 31.9 + - - +
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 2.7 47.1 + - - +
47A ALA* 3.7 10.1 - - - +
49A GLN* 1.3 75.2 - - + +
51A ILE* 1.3 63.5 + - - +
53A HIS* 4.0 4.6 - - - +
54A ALA* 3.1 23.4 + - - +
74A LEU* 3.6 6.7 - - + +
79A GLN* 3.1 40.0 + - + +
82A GLU* 2.5 42.9 + - - +
83A ILE* 4.7 4.0 - - + -
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.0 23.1 - - + -
25A PHE* 4.5 4.9 - - + -
47A ALA 3.1 20.1 + - - +
48A HIS* 3.8 3.1 - - - +
50A LYS* 1.3 73.7 - - - +
52A PHE* 1.3 55.8 + - - +
54A ALA* 2.9 6.1 + - - +
55A MET* 2.7 44.5 + - - +
70A VAL* 4.5 10.3 - - + +
74A LEU* 4.2 6.1 - - + -
83A ILE* 3.5 35.7 - - + -
88A TYR* 4.4 5.2 - - + -
89A LEU* 3.6 28.0 - - + -
92A LEU* 4.0 14.1 - - + -
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.1 8.3 - - + -
21A LEU* 3.8 5.3 - - + +
31A LEU* 4.2 6.7 - - + -
34A ALA* 3.9 42.0 - - + -
35A SER* 3.9 4.9 - - - -
38A LEU* 3.7 19.5 - - + -
39A ILE 4.6 0.2 - - - -
40A PRO* 4.2 14.1 - - + -
43A PHE* 3.6 32.1 - + + -
48A HIS 2.9 20.1 + - - +
49A GLN 4.1 2.5 - - - +
51A ILE* 1.3 73.7 - - - +
53A HIS* 1.3 61.7 + - - +
55A MET* 3.4 36.3 - - + +
56A LEU* 3.1 45.5 + - + +
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Residues in contact with HIS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PRO* 3.8 26.2 - - + +
41A GLU* 6.1 0.2 - - - -
49A GLN 3.0 19.0 + - - +
50A LYS* 4.0 5.8 + - - +
52A PHE* 1.3 77.8 - - - +
54A ALA* 1.3 58.8 + - - +
56A LEU* 2.9 10.9 + - + +
57A ARG* 2.7 78.1 + - - +
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LYS 3.1 14.5 + - - +
51A ILE 2.9 7.7 + - - +
53A HIS* 1.3 75.7 + - - +
55A MET* 1.3 66.8 + - - +
57A ARG* 3.6 9.3 - - - +
58A VAL* 3.0 29.6 + - - +
70A VAL* 4.5 4.7 - - + -
73A GLU* 3.8 19.7 - - + +
74A LEU* 3.7 24.5 - - + +
77A SER* 5.7 1.8 - - - +
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Residues in contact with MET 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.7 17.9 - - + +
24A VAL* 3.4 41.7 - - + -
25A PHE* 4.9 9.4 - - - -
31A LEU* 3.9 9.9 - - + -
51A ILE* 2.7 30.6 + - + +
52A PHE* 3.4 40.8 - - + +
54A ALA* 1.3 74.0 - - - +
56A LEU* 1.3 61.4 + - - +
58A VAL* 3.4 3.8 + - - +
59A ALA* 3.1 19.9 + - - +
65A VAL* 3.6 31.4 - - + +
70A VAL* 4.5 9.3 - - + +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.8 10.5 - - + -
35A SER* 3.8 25.4 - - - +
38A LEU 5.1 1.3 - - - +
39A ILE* 5.4 0.7 - - + -
40A PRO* 4.4 15.9 - - + -
52A PHE* 3.1 42.3 + - + +
53A HIS* 2.9 12.1 + - + +
55A MET* 1.3 77.2 - - - +
57A ARG* 1.3 65.4 + - - +
58A VAL 3.1 2.2 - - - -
59A ALA* 3.0 10.9 + - + +
60A ASP* 3.0 34.9 + - - +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS* 2.7 65.8 + - + +
54A ALA* 3.6 8.3 - - - +
56A LEU* 1.3 73.0 - - - +
58A VAL* 1.3 59.5 + - - +
60A ASP* 3.6 13.5 + - + +
61A ARG* 3.5 23.6 + - - -
73A GLU* 3.6 23.9 + - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA 3.0 19.3 + - - +
55A MET 3.6 4.5 - - - +
57A ARG* 1.3 74.4 - - - +
59A ALA* 1.3 67.0 + - - +
60A ASP 2.9 2.4 + - - -
61A ARG* 3.1 28.6 + - - +
62A GLY* 3.3 7.6 - - - +
63A GLU* 3.7 13.9 - - + +
64A PRO 3.2 31.6 - - - +
65A VAL* 3.9 4.7 - - + -
69A THR* 3.8 24.0 - - + +
70A VAL* 4.7 2.7 - - + -
73A GLU* 3.7 25.4 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.8 29.6 - - + -
55A MET 3.1 6.2 + - - +
56A LEU* 3.0 14.5 + - + +
58A VAL* 1.3 76.8 - - - +
60A ASP* 1.3 57.5 + - - +
61A ARG* 2.8 9.6 + - - -
62A GLY 3.0 16.0 - - - +
65A VAL* 3.8 8.0 - - + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.0 27.2 + - - +
57A ARG* 3.7 11.9 - - + +
58A VAL 2.9 1.4 + - - -
59A ALA* 1.3 76.5 - - - +
61A ARG* 1.3 66.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il